Introduction to R and Rstudio

Artwork by @allison_horst

Wrangling

Is the reshaping or transforming of data into a format which is easier to work with

This is often the largest part of many analyses and data science

A note on tidy data

Tidyverse functions work best with tidy data:

1. Each variable forms a column.
2. Each observation forms a row.

(Broadly, this means long rather than wide tables)

{dplyr} package

• {dplyr} is a language for data manipulation

6 functions/verbs to start with

6 key verbs will help us gain a deeper understanding of our data sets.

Note summarise() can also be spelt summarize()

dplyr::arrange()
dplyr::filter()
dplyr::mutate()
dplyr::group_by()
# followed often by 
dplyr::ungroup()
dplyr::summarise()

Building with steps

These verbs aren’t used independently of each other.

Each can be a step in the code, like a recipe but can also be repeated.

A recipe starts with:

potato then
peel then
slice into medium sized pieces then
boil for 25 minutes then
mash

Recipe as code

The potato is the object in R terms and the steps are verbs or functions

Pipe

Q1. Which organisation provided the highest number of Mental Health (MH) beds?

arrange()

Reorder rows based on selected variable

beds_data |> 
  arrange(beds_av)

Descending data

We need descending order:

beds_data |> 
  arrange(desc(beds_av))

desc() works for text and numeric variables

Q2. Which 2 organisations provided the highest number of MH beds in September 2018?

filter()

The expression inside brackets should return TRUE or FALSE. We are choosing rows where this expression is TRUE.

beds_data |> 
  filter(date == "2018-09-01") 

A negative test of equality

To exclude and test where the expression is NOT equal !=

beds_data |> 
  filter(date != "2018-09-01") 

Ordered and filtered

beds_data  |> 
  arrange(desc(beds_av)) |> 
  filter(date == "2018-09-01") 

Find the top 2 organisations

This isn’t a key function but useful

beds_data  |> 
  arrange(desc(beds_av)) |> 
  filter(date == "2018-09-01") |> 
  slice_head(n = 2)

Q3. Which 5 organisations had the highest percentage bed occupancy in September 2018?

Create new variables

= in this context is an alias not a test of equality

beds_data |> 
  mutate(perc_occ = occ_av / beds_av) |> 
  filter(date == "2018-09-01") |> 
  arrange(desc(perc_occ)) 

Q4. What was the mean number of beds, (across all trusts) for each value of date?

summarise()

Collapses a single summary value

beds_data |> 
  summarise(mean_beds = mean(beds_av))

Missing values

We’ll need to remove NA values to get a suitable mean. TRUE can also be T

beds_data |> 
  summarise(mean_beds = mean(beds_av,
                             na.rm = TRUE)) 

Have a go!

Instead of mean() use median()

object |> 
  summarise(new_name = function_name(column_name,
                                     na.rm = ???))

Use a sum() statistic twice

object |> 
  summarise(col_1 = function_name(beds_av,
                                  na.rm = ???),
            col_2 = function_name(occ_av),
            na.rm = ???)
)

Answer for summary statistics

median()

beds_data |> 
  summarise(per_occ = median(beds_av,
                             na.rm = TRUE))

# A tibble: 1 × 1
  per_occ
    <dbl>
1     241

sum()

beds_data |> 
  summarise(total_beds = sum(beds_av, na.rm = TRUE),
            total_occupacy = sum(occ_av, na.rm = TRUE))

# A tibble: 1 × 2
  total_beds total_occupacy
       <dbl>          <dbl>
1     412480         368434

Applying summarise() to groups

group_by() - persistent grouping

group_by() does nothing to the output alone.
The change occurs behind the scenes.

beds_data |> 
  group_by(date) 

ungroup()

Seeing ungroup()

head() is the base R version of slice() and is unaffected by group_by()

beds_data |> 
  group_by(date) |> 
  head(1)

beds_data |> 
  group_by(date) |> 
  ungroup() |> 
  slice_head(n = 1)

Group by - in operation

The summarise() function currently relies upon the group_by() function to apply summary statistics to groups/sets but in a new release the reliance will be changed to be function specific. Currently code

beds_data |> 
  group_by(date) |>
  summarise(mean_beds = mean(beds_av, 
                             na.rm = TRUE))

Break?

Option to take this break before an exercise of after

Q5. Which 5 organisations have the highest mean % bed occupancy?

Hint

beds_data |> 
  group_by() |> 
  summarise() |>
  mutate() |> 
  arrange()

Solution

beds_data |> 
  group_by(org_name) |> 
  summarise(total_beds = sum(beds_av, na.rm = TRUE),
            total_occupancy = sum(occ_av, na.rm = TRUE)) |> 
  mutate(perc_occ = total_occupancy / total_beds) |> 
  arrange(desc(perc_occ))